It could be that mail is stored in ~/Mail now, but KMail somehow looks in ~/.kde/share/apps/kmail/mail . To make sure that KMail looks in the right directory, whichever that may be, you should edit your kmailrc.
Add the following line under the [General] section:
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Source code
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1
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folders=path-to-folder
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Make sure Kontact/KMail is not running at that point.